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build: false | ||
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environment: | ||
matrix: | ||
- PYTHON_VERSION: 2.7 | ||
MINICONDA: C:\Miniconda | ||
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init: | ||
- "ECHO %PYTHON_VERSION% %MINICONDA%" | ||
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install: | ||
- "set PATH=%MINICONDA%;%MINICONDA%\\Scripts;%PATH%" | ||
- conda config --set always_yes yes --set changeps1 no | ||
- conda update -q conda | ||
- "conda env create --force -f environment.yml python=2.7" | ||
- activate segmentator | ||
- python setup.py develop | ||
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test_script: | ||
- py.test |
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[run] | ||
source = segmentator | ||
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omit = | ||
*__init__* | ||
*__main__* | ||
*config* | ||
*tests/* | ||
segmentator/future/* |
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@@ -61,3 +61,5 @@ target/ | |
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#Ipython Notebook | ||
.ipynb_checkpoints | ||
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bin/ |
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sudo: false | ||
os: | ||
- linux | ||
- osx | ||
matrix: | ||
allow_failures: | ||
- os: osx | ||
language: python | ||
python: | ||
- 2.7 | ||
install: # command to install dependencies | ||
- pip install -r requirements.txt | ||
- python setup.py develop | ||
script: # command to run tests | ||
- py.test --cov=./segmentator | ||
after_success: | ||
- bash <(curl -s https://codecov.io/bash) | ||
notifications: | ||
email: false |
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# Segmentator | ||
[![DOI](https://zenodo.org/badge/59303623.svg)](https://zenodo.org/badge/latestdoi/59303623) [![Build Status](https://travis-ci.org/ofgulban/segmentator.svg?branch=master)](https://travis-ci.org/ofgulban/segmentator) [![Build status](https://ci.appveyor.com/api/projects/status/lkxp4y5ahssqv6ng?svg=true)](https://ci.appveyor.com/project/ofgulban/segmentator) [![codecov](https://codecov.io/gh/ofgulban/segmentator/branch/master/graph/badge.svg)](https://codecov.io/gh/ofgulban/segmentator) [![Code Health](https://landscape.io/github/ofgulban/segmentator/master/landscape.svg?style=flat)](https://landscape.io/github/ofgulban/segmentator/master) [![Gitter chat](https://badges.gitter.im/gitterHQ/gitter.png)](https://gitter.im/segmentator/Lobby) | ||
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[![DOI](https://zenodo.org/badge/59303623.svg)](https://zenodo.org/badge/latestdoi/59303623) | ||
[![Gitter chat](https://badges.gitter.im/gitterHQ/gitter.png)](https://gitter.im/segmentator/Lobby) | ||
# Segmentator | ||
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<img src="logo/logo.png" width=420 align="right" /> | ||
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Segmentator is a free and open-source package for multi-dimensional data exploration and segmentation for 3D images. This application is mainly developed and tested using ultra-high field magnetic resonance imaging (MRI) brain data. | ||
Segmentator is a free and open-source package for multi-dimensional data exploration and segmentation for 3D images. This application is mainly developed and tested using ultra-high field magnetic resonance imaging (MRI) brain data. | ||
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The goal is to provide a complementary tool to the already available brain tissue segmentation methods (to the best of our knowledge) in other software packages (FSL, Freesurfer, SPM, Brainvoyager, itk-SNAP, etc.). | ||
The goal is to provide a complementary tool to the already available brain tissue segmentation methods (to the best of our knowledge) in other software packages (FSL, Freesurfer, SPM, Brainvoyager, itk-SNAP, etc.). | ||
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## Core dependencies | ||
[**Python 2.7**](https://www.python.org/download/releases/2.7/) | ||
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| Package | Tested version | | ||
|--------------------------------------|----------------| | ||
| [NumPy](http://www.numpy.org/) | 1.11.1 | | ||
| [matplotlib](http://matplotlib.org/) | 1.5.3 | | ||
| [matplotlib](http://matplotlib.org/) | 2.0.2 | | ||
| [NumPy](http://www.numpy.org/) | 1.13.1 | | ||
| [NiBabel](http://nipy.org/nibabel/) | 2.1.0 | | ||
| [SciPy](http://scipy.org/) | 0.19.1 | | ||
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## Installation & Quick Start | ||
Please visit [our wiki](https://github.com/ofgulban/segmentator/wiki/Installation) to see how to install and use Segmentator. | ||
- Make sure you have [**Python 2.7**](https://www.python.org/download/releases/2.7/) and [**pip**](https://en.wikipedia.org/wiki/Pip_(package_manager)) installed. | ||
- Change directory in your command line: | ||
``` | ||
cd /path/to/segmentator | ||
``` | ||
- Install the requirements by running the following command: | ||
``` | ||
pip install -r requirements.txt | ||
``` | ||
- Install Segmentator: | ||
``` | ||
python setup.py install | ||
``` | ||
- Simply call segmentator with a nifti file: | ||
``` | ||
segmentator /path/to/file.nii.gz | ||
``` | ||
- Or see the help for available options: | ||
``` | ||
segmentator --help | ||
``` | ||
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Visit [our wiki](https://github.com/ofgulban/segmentator/wiki/Installation) to see alternative installation methods. | ||
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## Support | ||
Please use [GitHub issues](https://github.com/ofgulban/segmentator/issues) for questions, bug reports or feature requests. | ||
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## License | ||
The project is licensed under [GNU General Public License Version 3](http://www.gnu.org/licenses/gpl.html). | ||
Copyright © 2016, [Omer Faruk Gulban](https://github.com/ofgulban) and [Marian Schneider](https://github.com/MSchnei). | ||
Released under [GNU General Public License Version 3](http://www.gnu.org/licenses/gpl.html). | ||
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## References | ||
This application is based on the following work: | ||
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* Kindlmann, G., & Durkin, J. W. (1998). Semi-automatic generation of transfer functions for direct volume rendering. In Proceedings of the 1998 IEEE symposium on Volume visualization - VVS ’98 (pp. 79–86). New York, New York, USA: ACM Press. http://doi.org/10.1145/288126.288167 | ||
* Kniss, J., Kindlmann, G., & Hansen, C. (2001). Interactive volume rendering using multi-dimensional transfer functions and direct manipulation widgets. In Proceedings Visualization, 2001. VIS ’01. (pp. 255–562). IEEE. http://doi.org/10.1109/VISUAL.2001.964519 | ||
* Kniss, J., Kindlmann, G., & Hansen, C. (2002). Multidimensional transfer functions for interactive volume rendering. IEEE Transactions on Visualization and Computer Graphics, 8(3), 270–285. http://doi.org/10.1109/TVCG.2002.1021579 | ||
* Kniss, J., Kindlmann, G., & Hansen, C. D. (2005). Multidimensional transfer functions for volume rendering. Visualization Handbook, 189–209. http://doi.org/10.1016/B978-012387582-2/50011-3 | ||
* Jianbo Shi, & Malik, J. (2000). Normalized cuts and image segmentation. IEEE Transactions on Pattern Analysis and Machine Intelligence, 22(8), 888–905. http://doi.org/10.1109/34.868688 | ||
* Ip, C. Y., Varshney, A., & Jaja, J. (2012). Hierarchical exploration of volumes using multilevel segmentation of the intensity-gradient histograms. IEEE Transactions on Visualization and Computer Graphics, 18(12), 2355–2363. http://doi.org/10.1109/TVCG.2012.231 | ||
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* Kindlmann, G., & Durkin, J. W. (1998). Semi-automatic generation of transfer functions for direct volume rendering. In Proceedings of the 1998 IEEE symposium on Volume visualization - VVS ’98 (pp. 79–86). New York, New York, USA: ACM Press. http://doi.org/10.1145/288126.288167 | ||
* Kniss, J., Kindlmann, G., & Hansen, C. (2001). Interactive volume rendering using multi-dimensional transfer functions and direct manipulation widgets. In Proceedings Visualization, 2001. VIS ’01. (pp. 255–562). IEEE. http://doi.org/10.1109/VISUAL.2001.964519 | ||
* Kniss, J., Kindlmann, G., & Hansen, C. (2002). Multidimensional transfer functions for interactive volume rendering. IEEE Transactions on Visualization and Computer Graphics, 8(3), 270–285. http://doi.org/10.1109/TVCG.2002.1021579 | ||
* Kniss, J., Kindlmann, G., & Hansen, C. D. (2005). Multidimensional transfer functions for volume rendering. Visualization Handbook, 189–209. http://doi.org/10.1016/B978-012387582-2/50011-3 | ||
* Jianbo Shi, & Malik, J. (2000). Normalized cuts and image segmentation. IEEE Transactions on Pattern Analysis and Machine Intelligence, 22(8), 888–905. http://doi.org/10.1109/34.868688 | ||
* Ip, C. Y., Varshney, A., & Jaja, J. (2012). Hierarchical exploration of volumes using multilevel segmentation of the intensity-gradient histograms. IEEE Transactions on Visualization and Computer Graphics, 18(12), 2355–2363. http://doi.org/10.1109/TVCG.2012.231 |
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name: segmentator | ||
channels: | ||
- conda-forge | ||
dependencies: | ||
- setuptools>=19.6* | ||
- pytest>=3* | ||
- pytest-cov>=2.5* | ||
- numpy>=1.13* | ||
- scipy>=0.19* | ||
- matplotlib>=2.0* | ||
- nibabel>=2.1* |
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numpy==1.13.1 | ||
scipy==0.19.1 | ||
matplotlib==2.0.2 | ||
nibabel==2.1.0 | ||
pytest-cov==2.5.1 |
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"""All this stuff is to get the version from setup.py.""" | ||
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from pkg_resources import get_distribution, DistributionNotFound | ||
import os.path | ||
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try: | ||
_dist = get_distribution('segmentator') | ||
# Normalize case for Windows systems | ||
dist_loc = os.path.normcase(_dist.location) | ||
here = os.path.normcase(__file__) | ||
if not here.startswith(os.path.join(dist_loc, 'segmentator')): | ||
# not installed, but there is another version that *is* | ||
raise DistributionNotFound | ||
except DistributionNotFound: | ||
__version__ = 'Version information not found. Please install this project \ | ||
with setup.py)' | ||
else: | ||
__version__ = _dist.version |
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